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OpenMS
2.5.0
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66 const std::map<String, std::vector<double> > & getProtMasses()
const;
69 const std::vector<double> & getMasses(
String acc)
const;
71 const std::map<String, std::vector<double> > & getProteinRTMap()
const;
72 const std::map<String, std::vector<double> > & getProteinPTMap()
const;
73 const std::map<String, std::vector<String> > & getProteinPeptideSequenceMap()
const;
85 void dbPreprocessing(
String db_path,
bool save =
true);
98 void dbPreprocessing(
String db_path,
String rt_model_path,
String dt_model_path,
bool save =
true);
108 void loadPreprocessing();
111 double getWeight(
double mass);
113 double getRT(
String prot_id,
Size peptide_index);
115 double getPT(
String prot_id,
Size peptide_index);
117 void setFixedModifications(
StringList & modifications);
120 return fixed_modifications_;
123 void setGaussianParameters(
double mu,
double sigma);
135 double getRTProbability(
double pred_rt,
Feature & feature);
140 void savePreprocessedDBWithRT_(
String db_path,
String path);
142 void loadPreprocessedDB_(
String path);
145 Int getScanNumber_(
double rt);
146 double getRTProbability_(
double min_obs_rt,
double max_obs_rt,
double pred_rt);
148 void updateMembers_()
override;
const std::map< char, std::vector< String > > & getFixedModifications()
Definition: PrecursorIonSelectionPreprocessing.h:118
double getGaussMu()
Definition: PrecursorIonSelectionPreprocessing.h:124
double sigma_
Definition: PrecursorIonSelectionPreprocessing.h:168
std::map< String, std::vector< double > > rt_prot_map_
Definition: PrecursorIonSelectionPreprocessing.h:164
A more convenient string class.
Definition: String.h:58
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool fixed_mods_
Definition: PrecursorIonSelectionPreprocessing.h:163
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
std::set< AASequence > sequences_
the sequences of the tryptic peptides
Definition: PrecursorIonSelectionPreprocessing.h:153
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
double mu_
Definition: PrecursorIonSelectionPreprocessing.h:169
std::vector< UInt > counter_
counter for the bins
Definition: PrecursorIonSelectionPreprocessing.h:159
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::map< String, std::vector< String > > prot_peptide_seq_map_
Definition: PrecursorIonSelectionPreprocessing.h:166
std::vector< double > masses_
all tryptic masses of the distinct peptides in the database
Definition: PrecursorIonSelectionPreprocessing.h:151
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< double > bin_masses_
the masses of the bins used for preprocessing (only used if bins are not equidistant,...
Definition: PrecursorIonSelectionPreprocessing.h:157
An LC-MS feature.
Definition: Feature.h:70
double getGaussSigma()
Definition: PrecursorIonSelectionPreprocessing.h:129
std::map< String, std::vector< double > > prot_masses_
stores masses of tryptic peptides for proteins, key is the accession number
Definition: PrecursorIonSelectionPreprocessing.h:155
std::map< String, std::vector< double > > pt_prot_map_
Definition: PrecursorIonSelectionPreprocessing.h:165
UInt f_max_
maximal relative frequency of a mass
Definition: PrecursorIonSelectionPreprocessing.h:161
This class implements the database preprocessing needing for precursor ion selection.
Definition: PrecursorIonSelectionPreprocessing.h:55
std::map< char, std::vector< String > > fixed_modifications_
Definition: PrecursorIonSelectionPreprocessing.h:167